I never got the impression from Iron Man that SHIELD was a brand-new agency. The only evidence of that was Coulson saying "we're working on it" when Pepper said their name was a mouthful. To me, that only suggested that they'd changed the acronym, not that the agency was new. Although it has since been established by The Winter Soldier that the current full name was in use decades ago. So maybe "we're working on it" just meant they were thinking about changing the name. Or maybe it was just Coulson being Coulson.